[Biopython-dev] gsoc phylo project questions

[Yanbo Ye]

Hi Eric,

Again, thanks for your comment. It might be better to discuss here.
https://github.com/lijax/gsoc/commit/e969c82a5a0aef45bba1277ce01d6dbee03e6a84#commitcomment-3096321

I have changed my proposal and timeline based on your advice. I think I was
too optimistic that I didn't consider about the compatibility with existing
code or other potential problem that may exist. After careful
consideration, I removed one task from the goal list to make the time more
relaxed, the tree
comparison<http://www.biopython.org/wiki/Phylo_cookbook#Comparing_trees>(seems
I miss understood this). I might be able to complete all of them. But it's
better to make it as an extra task, to make sure this coding experience is
not a burden.

According to your comment:

1. I didn't know PyCogent and DendroPy. I'll refer to them for useful
solutions.
2. For distance-based tree and consensus tree, I think there is no need to
use NumPy. And for consensus tree, my original plan is to implement a
binary class to count the clade with the same leaves for performance. As
you suggest, I'll implement a class with the same API and improve the
performance later, so that I can pay more attention to the Strict and Adam
Consensus algorithms.
3. I didn't find the distance matrix method for MSA on Phylo Cookbook page,
only from existing tree.
4. For parsimony tree search, I have already know how several heuristic
search algorithms work. Do I need to implement them all?
5. I'm not clear about the radial layout and Felsenstein's Equal Daylight
algorithm. Isn't this algorithm one way of showing the radial layout? I'm
sorry that I'm not familiar with this layout. Can you give some figure
examples and references?

Best,

Yanbo
-- 

叶彦波

中科院武汉病毒所生物信息学课题组

Ye Yanbo

Bioinformatics Group, Wuhan Institute Of Virology, Chinese Academy of
Sciences